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Objective: Despite the causes for melanin increase, the increased gene expression of TYR is a common pathological process. Based on this viewpoint, antisense-S-Oligo of TYR was designed and synthesized to regulate synthesis of melanin in order to explore the treatment for skin pigmentation., Methods: The cultured melanocytes were divided into 3 groups. The group 1 was treated with endothelin, group 2 treated with ultraviolet ray and group 3 was used as the control. In each group, the 5' antisense-S-Oligo, the 3' antisense-S-Oligo, the mixed antisense-S-Oligo of TYR or Dotap only was added. The melanin content and TYR gene expressions were examined., Results: The 5' antisense-S-Oligo, the 3' antisense-S-Oligo and the mixed antisense-S-Oligo significantly inhibited the increase of melanin content and TYR gene expression, which were caused by endothelin or ultraviolet ray treatment. Of the three treatments, the 3' antisense-S-Oligo showed the strongest effect., Conclusion: Antisense-S-Oligo has significant regulating effects on TYR gene expression and melanin content. The 3' antisense-S-Oligo is more effective than the 5' antisense-S-Oligo.

The GLK gene family plays a crucial role in the regulation of chloroplast development and participates in chlorophyll synthesis. However, the precise mechanism by which GLK contributes to citrus's chlorophyll synthesis remains elusive. The GLK gene family causes variations in the photosynthetic capacity and chlorophyll synthesis of different citrus varieties. In this study, we identified tissue-specific members and the key CcGLKs involved in chlorophyll synthesis. A total of thirty CcGLK transcription factors (TFs) were discovered in the citrus genome, distributed across all nine chromosomes. The low occurrence of gene tandem duplication events and intronic variability suggests that intronic variation may be the primary mode of evolution for CcGLK TFs. Tissue-specific expression patterns were observed for various GLK family members; for instance, CcGLK12 and CcGLK15 were specifically expressed in the skin, while CcGLK30 was specific to the ovary, and CcGLK10, CcGLK6, CcGLK21, CcGLK2, CcGLK18, CcGLK9, CcGLK28, and CcGLK8 were specifically expressed in the leaves. CcGLK4, CcGLK5, CcGLK11, CcGLK23, CcGLKl7, CcGLK26, and CcGLK20 may participate in the regulation of the ALA, prochlorophylate, protoporphyrin IX, Mg-protoporphyrin IX, Chl b, T-Chl, MG-ProtoIX ME, and POR contents in citrus. [ABSTRACT FROM AUTHOR]

In bacteria, the Rho protein mediates Rho-dependent termination (RDT) by identifying a non-specific cytosine-rich Rho utilization site on the newly synthesized RNA. As a result of RDT, downstream RNA transcription is reduced. Due to the bias in reverse transcription and PCR amplification, we could not identify the RDT site by directly measuring the amount of mRNA upstream and downstream of RDT sites. To overcome this difficulty, we employed a 77 bp reporter gene argX, (coding tRNAarg) from Brevibacterium albidum, and we transcriptionally fused it to the sequences to be assayed. We constructed a series of plasmids by combining a segment of the galactose (gal) operon sequences, both with and without the RDT regions at the ends of cistrons (galE, galT, and galM) upstream of argX. The RNA polymerase will transcribe the gal operon sequence and argX unless it encounters the RDT encoded by the inserted sequence. Since the quantitative real-time PCR (qRT-PCR) method detects the steady state following mRNA synthesis and degradation, we observed that tRNAarg is degraded at the same rate in these transcriptional fusion plasmids. Therefore, the amount of tRNAarg can directly reflect the mRNA synthesis. Using this approach, we were able to effectively assay the RDTs and Rho-independent termination (RIT) in the gal operon by quantifying the relative amount of tRNAarg using qRT-PCR analyses. The resultant RDT% for galET, galTK, and at the end of galM were 36, 26, and 63, individually. The resultant RIT% at the end of the gal operon is 33%. Our findings demonstrate that combining tRNAarg with qRT-PCR can directly measure RIT, RDT, or any other signal that attenuates transcription efficiencies in vivo, making it a useful tool for gene expression research. [ABSTRACT FROM AUTHOR]

Recently, there has been growing interest among researchers in exploring the effects of epithelial-mesenchymal transformation (EMT) or N6-Methyladenosine (m6A) modification regulators on tumor development. However, the synergistic efficiency of these regulators in relation to ovarian cancer development remains unclear. This study aims to explore the transcription patterns of main regulators, including 19 EMT and 22 m6A, in ovarian cancer samples from TCGA datasets and normal samples from GTEx datasets. After conducting a LASSO regression analysis, ten prognostic signatures were identified, namely KIAA1429, WTAP, SNAI1, AXL, IGF2BP1, ELAVL1, CBLL1, CDH2, NANOG and ALKBH5. These signatures were found to have a comprehensive effect on immune infiltrating signatures and the final prognostic outcome. Next, utilizing the ssGSEA algorithm and conducting overall survival analyses, we have identified the key prognosis-related immunological signatures in ovarian cancer to be ALKBH5, WTAP, ELAVL1, and CDH2 as the regulators. The characteristic immune response and related genetic expression have revealed a significant correlation between the alteration of m6A regulators and EMT regulators, indicating a synergistic effect between these two factors in the development of ovarian cancer. In summary, our research offers a novel perspective and strategy to enhance the occurrence, progression, and prognosis of ovarian cancer. [ABSTRACT FROM AUTHOR]

Single-cell RNA sequencing (RNA-seq) has been demonstrated to be a proven method for quantifying gene-expression heterogeneity and providing insight into the transcriptome at the single-cell level. When combining multiple single-cell transcriptome datasets for analysis, it is common to first correct the batch effect. Most of the state-of-the-art processing methods are unsupervised, i.e., they do not utilize single-cell cluster labeling information, which could improve the performance of batch correction methods, especially in the case of multiple cell types. To better utilize known labels for complex dataset scenarios, we propose a novel deep learning model named IMAAE (i.e., integrating multiple single-cell datasets via an adversarial autoencoder) to correct the batch effects. After conducting experiments with various dataset scenarios, the results show that IMAAE outperforms existing methods for both qualitative measures and quantitative evaluation. In addition, IMAAE is able to retain both corrected dimension reduction data and corrected gene expression data. These features make it a potential new option for large-scale single-cell gene expression data analysis. [ABSTRACT FROM AUTHOR]

Simple Summary: Lung adenocarcinoma (LADC) is the pathological type with the highest morbidity and mortality among lung cancers. Although achievements in new therapeutic approaches have been developed, chemotherapy is still the most widely choice for control of LADC. However, the increasing drug resistance becomes the major challenge, so the development of the novel and efficient chemotherapeutic drug is still urgent. Elaiophylin, a new type of autophagy inhibitor, has been shown to possess unique anti-cancer activity. In this study, we have deeply investigated the therapeutic effect of elaiophylin on LADC and found elaiophylin exerts its anti-cancer effect though inhibiting mitophagy and oxidative stress and targeting SIRT1/Nrf2 signaling. This innovative and comprehensive research may provide the possibility for the development of novel chemotherapy drug for LADC. Lung adenocarcinoma (LADC), the most common type of lung cancer, is still one of the most aggressive and rapidly fatal tumor types, even though achievements in new therapeutic approaches have been developed. Elaiophylin as a C2 symmetrically glycosylated 16 macrolides has been reported to be a late-stage autophagy inhibitor with a potent anti-tumor effect on various cancers. This study investigated the anti-tumor effect of elaiophylin on human LADC for the first time in in vitro and in vivo models. The in vitro study in LADC A549 cells showed that elaiophylin significantly inhibited cell viability and induced cell apoptosis through the suppression of mitophagy and induction of cellular and mitochondrial oxidative stress. Proteomic analysis and molecular docking assay implicated that SIRT1 was likely the direct target of elaiophylin in A549 cells. Further mechanistic study verified that elaiophylin reduced Nrf2 deacetylation, expression, and transcriptional activity as well as cytoplasm translocation by downregulating SIRT1 expression and deacetylase activity. Additionally, SIRT1/Nrf2 activation could attenuate elaiophylin-induced mitophagy inhibition and oxidative stress. The in vivo study in the A549-xenograft mice model showed that the anti-tumor effect of elaiophylin was accompanied by the decreased expressions of SIRT1, Nrf2, Parkin, and PINK1. Thus, the present study reports that elaiophylin has potent anti-tumor properties in LADC, which effect is likely mediated through suppressing the SIRT1/Nrf2 signaling. In conclusion, elaiophylin may be a novel drug candidate for LADC and SIRT1 may be a new therapeutic target for such devastating malignancy. [ABSTRACT FROM AUTHOR]

The breast muscle is essential for flight and determines the meat yield and quality of the meat type in pigeons. At present, studies about long non-coding RNA (lncRNA) expression profiles in skeletal muscles across the postnatal development of pigeons have not been reported. Here, we used transcriptome sequencing to examine the White-King pigeon breast muscle at four different ages (1 day, 14 days, 28 days, and 2 years old). We identified 12,918 mRNAs and 9158 lncRNAs (5492 known lncRNAs and 3666 novel lncRNAs) in the breast muscle, and 7352 mRNAs and 4494 lncRNAs were differentially expressed in the process of development. We found that highly expressed mRNAs were mainly related to cell-basic and muscle-specific functions. Differential expression and time-series analysis showed that differentially expressed genes were primarily associated with muscle development and functions, blood vessel development, cell cycle, and energy metabolism. To further predict the possible role of lncRNAs, we also conducted the WGCNA and trans/cis analyses. We found that differentially expressed lncRNAs such as lncRNA-LOC102093252, lncRNA-G12653, lncRNA-LOC110357465, lncRNA-G14790, and lncRNA-LOC110360188 might respectively target UBE2B, Pax7, AGTR2, HDAC1, Sox8 and participate in the development of the muscle. Our study provides a valuable resource for studying the lncRNAs and mRNAs of pigeon muscles and for improving the understanding of molecular mechanisms in muscle development. [ABSTRACT FROM AUTHOR]

Salt stress is a critical limiting factor for fruit yield and quality of apples. Brassinosteroids (BRs) play an important role in response to abiotic stresses. In the present study, application of 2,4- Epicastasterone on seedlings of Malus 'M9T337' and Malus domestica 'Gala3' alleviated the physiological effects, such as growth inhibition and leaf yellowing, induced by salt stress. Further analysis revealed that treatment with NaCl induced expression of genes involved in BR biosynthesis in 'M9T337' and 'Gala3'. Among which, the expression of BR biosynthetic gene MdBR6OX2 showed a three-fold upregulation upon salt treatment, suggesting its potential role in response to salt stress in apple. MdBR6OX2, belonging to the CYP450 family, contains a signal peptide region and a P450 domain. Expression patterns analysis showed that the expression of MdBR6OX2 can be significantly induced by different abiotic stresses. Overexpressing MdBR6OX2 enhanced the tolerance of apple callis to salt stress, and the contents of endogenous BR-related compounds, such as Typhastero (TY), Castasterone (CS) and Brassinolide (BL) were significantly increased in transgenic calli compared with that of wild-type. Extopic expression of MdBR6OX2 enhanced tolerance to salt stress in Arabidopsis. Genes associated with salt stress were significantly up-regulated, and the contents of BR-related compounds were significantly elevated under salt stress. Our data revealed that BR-biosynthetic gene MdBR6OX2 positively regulates salt stress tolerance in both apple calli and Arabidopsis. • Exogenous application of BR alleviates salt-induced stress responses in Malus spp. • MdBR6OX2 positively regulates salt stress tolerance in both apple and Arabidopsis. • MdBR6OX2 is involved in BR biosynthesis in plants. [ABSTRACT FROM AUTHOR]

Fish culture in paddy fields is a traditional aquaculture mode, which has a long history in East Asia. Large-scale loach (Paramisgurnus dabryanus) fast growth is suitable for paddy fields aquaculture in China. The objective of this study was to identify differential expression genes (DEGs) in the brain, liver and muscle tissues between large (LG, top 5% of maximum total length) and small (SG, top 5% of minimum total length) groups using RNA-seq. In total, 150 fish were collected each week and 450 fish were collected at twelfth week from three paddy fields for all the experimental. Histological observation found that the muscle fibre diameter of LG loaches was greater than that of SG loaches. Transcriptome results revealed that the high expression genes (HEGs) in LG loaches (fold change ≥ 2, p < 0.05) were mainly concentrated in metabolic pathways, such as "Thyroid hormone signalling pathway", "Citrate cycle (TCA cycle)", "Carbon metabolism", "Fatty acid metabolism", and "Cholesterol metabolism", and the HEGs in SG loaches were enriched in the pathways related to environmental information processing such as "Cell adhesion molecules (CAMs)", "ECM− receptor interaction" and "Rap1 signalling pathway"; cellular processes such as "Tight junction", "Focal adhesion", "Phagosome" and "Adherens junction". Furthermore, IGFs gene family may play an important role in loach growth for their different expression pattern between the two groups. These findings can enhance our understanding about the molecular mechanism of different growth and development levels of loaches in paddy fields. [ABSTRACT FROM AUTHOR]

Purpose/aim of the study: To conduct a survey spectrum of the PITX2, FOXC1, and PRDM5 genes to reveal genotype-phenotype correlations in a cohort of Southeastern Chinese patients with Axenfeld-Rieger syndrome (ARS). Materials and methods: A total of 20 probands with ARS were recruited in Southeast China. All patients underwent full ocular and systemic examinations. Sanger sequencing was used to analyze all coding regions of and regions adjacent to PITX2, FOXC1, and PRDM5 and 13 upstream regulatory elements of PITX2. Multiplex ligation-dependent probe amplification was performed to detect gross insertions and deletions in PITX2 and FOXC1. Quantitative polymerase chain reaction was used to detect copy number variations in regulatory elements of PITX2. A bioinformatics analysis was conducted to evaluate the pathogenicity of variants. Results: Eleven mutations, including eight novel mutations, were identified in PITX2. Seven of the mutations were truncations. A genotype-phenotype correlation analysis showed that 81.8% (9/11) of patients with mutations in PITX2 developed glaucoma before reaching 10 years old. The proportion of patients without detected mutations was only 33.3% (3/9, P = 0.0399). In patient G1399, ultrasound biomicroscopy revealed that the left eye exhibited a phenotype similar to aniridia with complete angle closure and a remaining stub of iris tissue. Conclusion: This is the first genetic study of a cohort of Southeastern Chinese patients with ARS. Eight novel mutations were detected, expanding the mutation spectrum of PITX2. PITX2 may be a major candidate gene for ARS in Southeastern Chinese patients. Truncations may be the primary mutation type in PITX2. Glaucoma onset may be earlier in patients with mutations in PITX2 than in those without mutations in PITX2 and FOXC1. A block of the anterior chamber angle by the end of the iris might represent the main factor influencing the development of glaucoma in ARS patients with an asymmetric aniridia phenotype. [ABSTRACT FROM AUTHOR]

Abstract: Malignant glioma is one of the most challenging central nervous system diseases to treat and has high rates of recurrence and mortality. Current therapies often fail to control tumor progression or improve patient survival. Marinobufagenin (MBG) is an endogenous mammalian cardiotonic steroid involved in sodium pump inhibition. Currently, various studies have indicated the potential of MBG in cancer treatments; however, the precise mechanisms are poorly understood. The functions of MBG were examined using colony formation, migration, cell cycle, and apoptosis assays in glioma cells. A mitochondrial membrane potential assay was performed to determine the mitochondrial transmembrane potential change, and cytochrome c release from mitochondria was assayed by fluorescence microscopy. An immunofluorescence assay was performed, and the nuclear translocation of NF‐κB in glioma cells was confirmed by confocal microscopy. Western blotting and RT‐qPCR were used to detect the protein and gene expression levels, respectively. In addition, transfection experiment of ATP1A1‐siRNA was further carried out to confirm the role of sodium pump α1 subunit in the anticancer effect of MBG in human glioma. The apoptosis‐promoting and anti‐inflammatory effects of MBG were further investigated, and the sodium pump α1 subunit and the ERK signaling pathway were found to be involved in the anticancer effect of MBG. The in vivo anticancer efficacy of MBG was also tested in xenografts in nude mice. Thus, therapies targeting the ERK signaling‐mediated mitochondrial apoptotic pathways regulated by MBG might represent potential treatments for human glioma, and this study could accelerate the finding of newer therapeutic approaches for malignant glioma treatment. [ABSTRACT FROM AUTHOR]

Genome-wide transcriptomic studies in humans and mice have become extensive and mature. However, a comprehensive and systematic understanding of protein-coding genes and long non-coding RNAs (lncRNAs) expressed during pig spleen development has not been achieved. LncRNAs are known to participate in regulatory networks for an array of biological processes. Here, we constructed 18 RNA libraries from developing fetal pig spleen (55 days before birth), postnatal pig spleens (0, 30, 180 days and 2 years after birth), and the samples from the 2-year-old Wild Boar. A total of 15,040 lncRNA transcripts were identified among these samples. We found that the temporal expression pattern of lncRNAs was more restricted than observed for protein-coding genes. Time-series analysis showed two large modules for protein-coding genes and lncRNAs. The up-regulated module was enriched for genes related to immune and inflammatory function, while the down-regulated module was enriched for cell proliferation processes such as cell division and DNA replication. Co-expression networks indicated the functional relatedness between protein-coding genes and lncRNAs, which were enriched for similar functions over the series of time points examined. We identified numerous differentially expressed protein-coding genes and lncRNAs in all five developmental stages. Notably, ceruloplasmin precursor (CP), a protein-coding gene participating in antioxidant and iron transport processes, was differentially expressed in all stages. This study provides the first catalog of the developing pig spleen, and contributes to a fuller understanding of the molecular mechanisms underpinning mammalian spleen development. [ABSTRACT FROM AUTHOR]

To elucidate metabolism of ascorbic acid (AsA) in sweet cherry fruit (Prunus avium ‘Hongdeng’), we quantified AsA concentration, cloned sequences involved in AsA metabolism and investigated their mRNA expression levels, and determined the activity levels of selected enzymes during fruit development and maturation. We found that AsA concentration was highest at the petal-fall period (0 days after anthesis) and decreased progressively during ripening, but with a slight increase at maturity. AsA did nevertheless continue to accumulate over time because of the increase in fruit fresh weight. Full-length cDNAs of 10 genes involved in the L-galactose pathway of AsA biosynthesis and 10 involved in recycling were obtained. Gene expression patterns of GDP-L-galactose phosphorylase (GGP2), L-galactono-1, 4-lactone dehydrogenase (GalLDH), ascorbate peroxidase (APX3), ascorbate oxidase (AO2), glutathione reductase (GR1), and dehydroascorbate reductase (DHAR1) were in accordance with the AsA concentration pattern during fruit development, indicating that genes involved in ascorbic acid biosynthesis, degradation, and recycling worked in concert to regulate ascorbic acid accumulation in sweet cherry fruit. [ABSTRACT FROM AUTHOR]

Background: Sortase A (SrtA) is a transpeptidase found in Staphylococcus aureus, which is widely used in site-specific protein modification. However, SrtA was expressed in Escherichia coli ( E. coli) in rather low level (ranging from several milligrams to 76.9 mg/L at most). The present study aims to optimize fermentation conditions for improving SrtA expression in E. coli. Results: Under the optimized media (0.48 g/L glycerol, 1.37 g/L tryptone, 0.51 g/L yeast extract, MOPS 0.5 g/L, PBS buffer 180 mL/L) and condition (30 °C for 8 h) in a 7-L fermentor, the enzyme activity and the yield of SrtA reached 2458.4 ± 115.9 U/mg DCW and 232.4 ± 21.1 mg/L, respectively, which were higher by 5.8- and 4.5-folds compared with initial conditions, respectively. The yield of SrtA also represented threefold increase than the previously reported maximal level. In addition, the enzymatic characterizations of SrtA (optimal temperature, optimal pH, the influence of metal irons, and tolerance to water-soluble organic solvents) were determined. Conclusions: Enhanced expression of SrtA was achieved by optimization of medium and condition. This result will have potential application for production levels of SrtA on an industry scale. Moreover, the detailed enzymatic characterizations of SrtA were examined, which will provide a useful guide for its future application. [ABSTRACT FROM AUTHOR]

Vascular endothelial growth factor (VEGF) B belongs to the VEGF family, but in contrast to VEGF-A, VEGF-B does not regulate blood vessel growth. Instead, VEGF-B controls endothelial fatty acid (FA) uptake and was identified as a target for the treatment of type 2 diabetes. The regulatory mechanisms controlling Vegfb expression have remained unidentified. We show that peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) together with estrogen-related receptor α (ERR-α) regulates expression of Vegfb Mice overexpressing PGC-1α under the muscle creatine kinase promoter (MPGC-1αTG mice) displayed increased Vegfb expression, and this was accompanied by increased muscular lipid accumulation. Ablation of Vegfb in MPGC-1αTG mice fed a high-fat diet (HFD) normalized glucose intolerance, insulin resistance, and dyslipidemia. We suggest that VEGF-B is the missing link between PGC-1α overexpression and the development of the diabetes-like phenotype in HFD-fed MPGC-1αTG mice. The findings identify Vegfb as a novel gene regulated by the PGC-1α/ERR-α signaling pathway. Furthermore, the study highlights the role of PGC-1α as a master metabolic sensor that by regulating the expression levels of Vegfa and Vegfb coordinates blood vessel growth and FA uptake with mitochondrial FA oxidation. [ABSTRACT FROM AUTHOR]

• 11 MdAAP genes were identified in Apple. • Members of each subgroup shared similar gene structure and motif arrangement, implying similar functions. • MdAAP4 may play an important role in abiotic stress and nitrogen deficiency. Amino acid permeases (AAPs) play important roles in plant amino acid transport and nitrogen metabolism. In this study, we carried a comprehensive analysis for apple genes encoding AAPs using bioinformatics and molecular biology. Eleven MdAAPs were identified by a genome-wide search and comparative genomic analysis revealed relatively conserved gene composition, transmembrane characteristics, and protein structures. Phylogenetic tree construction and analysis of the conserved motifs of MdAAPs and AtAAPs showed that AAPs can be classified into three groups (I, II, and III). We compared the promoters of the identified genes and did gene functional annotation and qRT-PCR and found a relationship between apple AAPs and nitrogen deficiency. The expression profile data implied that MdAAPs exhibit diversified distributions and functions in different tissues. [ABSTRACT FROM AUTHOR]

Motif finding problems, abstracted as the planted ( l, d)-motif finding problem, are a major task in molecular biology-finding functioning units and genes. In 2002, the random projection algorithm was introduced to solve the challenging (15, 4)-motif finding problem by using randomly chosen templates. Two years later, a so-called uniform projection algorithm was developed to improve the random projection algorithm by means of low-dispersion sequences generated by coverings. In this article, we introduce an improved projection algorithm called the low-dispersion projection algorithm, which uses low-dispersion sequences generated by developed almost difference families. Compared with the random projection algorithm, the low-dispersion projection algorithm can solve the ( l, d)-motif finding problem with fewer templates without decreasing the success rate. [ABSTRACT FROM AUTHOR]

There is a strong need to eliminate batch-specific differences when integrating single-cell RNA-sequencing (scRNA-seq) datasets generated under different experimental conditions for downstream task analysis. Existing batch correction methods usually transform different batches of cells into one preselected "anchor" batch or a low-dimensional embedding space, and cannot take full advantage of useful information from multiple sources. We present a novel framework, called IMGG, i.e., integrating multiple single-cell datasets through connected graphs and generative adversarial networks (GAN) to eliminate nonbiological differences between different batches. Compared with current methods, IMGG shows excellent performance on a variety of evaluation metrics, and the IMGG-corrected gene expression data incorporate features from multiple batches, allowing for downstream tasks such as differential gene expression analysis. [ABSTRACT FROM AUTHOR]

Aim:Gefitinib is effective in only approximately 20% of patients with non-small-cell lung cancer (NSCLC), and the underlying mechanism remains unclear. FoxM1 is upregulated in NSCLC and associated with a poor prognosis in NSCLC patients. In this study, we examined the possible role of FoxM1 in gefitinib resistance and the related mechanisms.Methods:Gefitinib resistant human lung adenocarcinoma cell line SPC-A-1 and gefitinib-sensitive human lung mucoepidermoid carcinoma cell line NCI-H292 were used. mRNA and protein expression of FoxM1 and other factors were tested with quantitative RT PCR and Western blot analysis. RNA interference was performed to suppress FoxM1 expression in SPC-A-1 cells, and lentiviral infection was used to overexpress FoxM1 in H292 cells. MTT assay and flow cytometry were used to examine the proliferation and apoptosis of the cells.Results:Treatment of SPC-A-1 cells with gefitinib (1 and 10 μmol/L) upregulated the expression of FoxM1 in time- and concentration-dependent manners, while gefitinib (1 μmol/L) downregulated in H292 cells. In SPC-A-1 cells treated with gefitinib (1 μmol/L), the expression of several downstream targets of FoxM1, including survivin, cyclin B1, SKP2, PLK1, Aurora B kinase and CDC25B, were significantly upregulated. Overexpression of FoxM1 increased the resistance in H292 cells, while attenuated FoxM1 expression restored the sensitivity to gefitinib in SPC-A-1 cells by inhibiting proliferation and inducing apoptosis.Conclusion:The results suggest that FoxM1 plays an important role in the resistance of NSCLC cells to gefitinib in vitro. FoxM1 could be used as a therapeutic target to overcome the resistance to gefitinib. [ABSTRACT FROM AUTHOR]

Abstract: Certain tumor cells and most tumor endothelial cells overexpress a membrane-spanning molecule, aminopeptidase N (CD13) isoform, which is the receptor for peptides containing the Asn–Gly–Arg (NGR) motif. NGR-modified docetaxel (DTX)-loaded PEG-b-PLA polymeric micelles (NGR–PM-DTX) were firstly developed and tested in vitro and in vivo, while DTX-loaded polymeric micelles (PM-DTX) and free DTX were used as controls. The NGR–PM-DTX containing DTX were about 35 nm in diameter with spherical shape and high encapsulation efficiency. It was demonstrated quantitatively by the spectrophotofluorometry and qualitatively by the confocal image analysis that NGR facilitates the uptake of micelles by CD13-overexpressed tumor cells (fibrosarcoma, HT1080) and endothelial cells (human umbilical vein endothelial cells, HUVEC). Free NGR inhibited cellular uptake of NGR–PM-DTX, revealing the mechanism of receptor-mediated endocytosis. Higher cytotoxicity toward HT1080 cells and more efficient inhibition of HUVEC proliferation were also observed in NGR–PM-DTX groups, which were consistent well with the observation of cellular uptake. In BALB/c mice bearing HT1080 tumor xenografts, stronger antitumor efficacy and less body weight changes were shown in NGR–PM-DTX group, with good correlation between in vitro and in vivo. Therefore, it was concluded that NGR-PM could be a potential vehicle for delivering hydrophobic chemotherapeutic agents to CD13-overexpressing tumors. [Copyright &y& Elsevier]

Different Arabidopsis phytochrome (phy) family members (phyA through phyE) display differential photosensory and/or physiological functions in regulating growth and developmental responses to light signals. To identify the genes regulated by phyB in response to continuous monochromatic red light (Rc) during the induction of seedling de-etiolation, we have performed time-course, microarray-based expression profiling of wild type (WT) and phyB null mutants. Comparison of the observed expression patterns with those induced by continuous monochromatic far-red light (FRc; perceived exclusively by phyA) in WT and phyA null-mutant seedlings suggests early convergence of the FRc and Rc photosensory pathways to control a largely common transcriptional network. phyB mutant seedlings retain a surprisingly high level of responsiveness to Rc for the majority of Rc-regulated genes on the microarray, indicating that one or more other phys have a major role in regulating their expression. Combined with the robust visible morphogenic phenotype of the phyB mutant in Rc, these data suggest that different members of the phy family act in organ-specific fashion in regulating seedling de-etiolation. Specifically, phyB appears to be the dominant, if not exclusive, photoreceptor in regulating a minority population of genes involved in suppression of hypocotyl cell elongation in response to Rc signals. By contrast, this sensory function is apparently shared by one or more other phys in regulating the majority Rc-responsive gene set involved in other important facets of the de-etiolation process in the apical region, such as cotyledon cell expansion. [ABSTRACT FROM AUTHOR]

Cereal grains accumulate carbohydrates, storage proteins and fatty acids via different pathways during their development. Many genes that participate in nutrient partitioning during grain filling and that affect starch quality have been identified. To understand how the expression of these genes is coordinated during grain development, a genomic approach to surveying the participation and interactions of all the pathways is necessary. Using recently published rice genome information, we designed a rice GeneChip microarray that covers half the rice genome. By monitoring the expression of 21 000 genes in parallel, we identified genes involved in the grain filling process and found that the expression of genes involved in different pathways is coordinately controlled in a synchronized fashion during grain filling. Interestingly, a known promoter element in genes encoding seed storage proteins, AACA, is statistically over-represented among the 269 genes in different pathways with diverse functions that are significantly up-regulated during grain filling. By expression pattern matching, a group of transcription factors that have the potential to interact with this element was identified. We also found that most genes in the starch biosynthetic pathway show multiple distinct spatial and temporal expression patterns, suggesting that different isoforms of a given enzyme are expressed in different tissues and at different developmental stages. Our results reveal key regulatory machinery and provide an opportunity for modifying multiple pathways by manipulating key regulatory elements for improving grain quality and quantity. [ABSTRACT FROM AUTHOR]

The transcription factor GATA-1 and its cofactor FOG-1 are essential for the normal development of erythroid cells and megakaryocytes. FOG-1 can stimulate or inhibit GATA-1 activity depending on cell and promoter context. How the GATA-1-FOG-1 complex controls the expression of distinct sets of gene in megakaryocytes and erythroid cells is not understood. Here, we examine the molecular basis for the megakaryocyte-restricted activation of the αIIb gene. FOG-1 stimulates GATA-1-dependent αIIb gene expression in a manner that requires their direct physical interaction. Transcriptional output by the GATA-1-FOG-1 complex is determined by the hematopoietic Ets protein Fli-1 that binds to an adjacent Ets element. Chromatin immunoprecipitation experiments show that GATA-1, FOG-1 and Fli-1 co-occupy the αIIb promoter in vivo. Expression of several additional megakaryocyte-specific genes that bear tandem GATA and Ets elements in their promoters also depends on the physical interaction between GATA-1 and FOG-1. Our studies define a molecular context for transcriptional activation by GATA-1 and FOG-1, and may explain the occurrence of tandem GATA and Ets elements in the promoters of numerous megakaryocyte-expressed genes. [ABSTRACT FROM AUTHOR]

For adaptation to challenging environments, plants have evolved various response mechanisms, such as inducing the expression of many stress genes, thereby increasing the resistance. Accelerated cell death (ACD) genes have been widely studied in plant senescence and defense responses. However, there are few reports on the role of ACD genes in abiotic stresses in plants. In this experiment, ACD11 was successfully isolated from apples (Malus baccata) and found to be mainly expressed in apple fruits and roots. The response elements of abiotic stresses were also found in the promoter of MbACD11. Furthermore, MbACD11 expression was induced by various abiotic stresses, especially salt treatment. After overexpression of MbACD11 in apple seedlings, callis and Arabidopsis thaliana , all showed enhanced tolerance to salt stress. Under salt conditions, MbACD11 -OE showed higher fresh weight and chlorophyll content compared to the WT. It also exhibited lower relative electrical conductivity, malondialdehyde (MDA) content, and reactive oxygen species (ROS) accumulation than the WT. The expression of salt stress-related genes was higher in MbACD11 -OE apple seedlings than in WT. In salt stress condition, the apple MbACD11 gene reduced ROS accumulation and affected the expression of salt stress-related genes, hence enhancing tolerance. • The MbACD11 enhances salt tolerance in apple by regulating the PCD gene. • MbACD11 alleviates oxidative stress such as that caused by ROS accumulation and enhances salt resistance in apple. • MbACD11 increases the expression of salt tolerance-related genes to enhance salt tolerance in apple. • MbACD11 ectopically overexpressed improves salt tolerance in Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Phytochrome-interacting factors (PIFs), members of the basic helix-loop-helix transcription factor family that have been extensively investigated in Arabidopsis thaliana, play essential roles in plant growth and development. However, PIF members have not been systematically investigated in apples, a worldwide perennial woody crop of economic importance. Here, seven PIF genes were identified from the Malus × domestica reference genome. Chromosomal locations, gene structures, and phylogenetic relationships of these members were analyzed. Analysis of cis-acting elements in promoter regions of MdPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Subsequently, subcellular localization and transcriptional activity analysis revealed that MdPIFs were typical nuclear transcription factors with transcriptional activation ability. Expression analysis demonstrated that MdPIF genes had different gene expression patterns for various abiotic factors. Moreover, overexpressed MdPIF4 reduced the sensitivity of apple calluses to abscisic acid (ABA). Our work lays foundations for further investigation of PIF functions in plant growth and development in apples. [ABSTRACT FROM AUTHOR]

A novel recombinant strain has been constructed for converting glycerol into a specific conjugated linoleic acid isomer (trans-10, cis-12 CLA) using Yarrowia lipolytica as host. The lipid accumulation pathway was modified for increasing lipid content. Overexpression of the diacylglycerol transferase (DGA1) gene improved the intracellular lipid yield by approximately 45% as compared to the original strain. The corresponding intracellular lipid yield of recombinant strain WXYL037 reached 52.2% of the cell dry weight. In combination with integration of Δ12 desaturase from Mortierella alpina (MA12D) and DGA1, the linoleic acid (LA) production content reached 0.88 g/L, which was 2-fold that of the original strain. Furthermore, with overexpressed DGA1, MA12D and Propionibacterium acnes isomerase (PAI), the titer of trans-10, cis-12 CLA in WXYL037 reached 110.6 mg/L after 72 h of shake flask culture, representing a 201.8% improvement when compared with that attained in the WXYL030 strain, which manifested overexpressed PAI. With optimal medium, the maximum CLA content and lipid yield of Y. lipolytica Po1g were 132.6 mg/L and 2.58 g/L, respectively. This is the first report of the production of trans-10, cis-12 CLA by the oleaginous yeast Y. lipolytica using glycerol as the sole carbon source through expression of DGA1 combined with MA12D and PAI. [ABSTRACT FROM AUTHOR]

Lung tissue plays an important role in the respiratory system of mammals after birth. Early lung development includes six key stages, of which the saccular stage spans the pre- and neonatal periods and prepares the distal lung for alveolarization and gas-exchange. However, little is known about the changes in gene expression between fetal and neonatal lungs. In this study, we performed transcriptomic analysis of messenger RNA (mRNA) and long noncoding RNA (lncRNA) expressed in the lung tissue of fetal and neonatal piglets. A total of 19,310 lncRNAs and 14,579 mRNAs were identified and substantially expressed. Furthermore, 3248 mRNAs were significantly (FDR-adjusted p value ≤ 0.05, FDR: False Discovery Rate) differentially expressed and were mainly enriched in categories related to cell proliferation, immune response, hypoxia response, and mitochondrial activation. For example, CCNA2, an important gene involved in the cell cycle and DNA replication, was upregulated in neonatal lungs. We also identified 452 significantly (FDR-adjusted p value ≤ 0.05) differentially expressed lncRNAs, which might function in cell proliferation, mitochondrial activation, and immune response, similar to the differentially expressed mRNAs. These results suggest that differentially expressed mRNAs and lncRNAs might co-regulate lung development in early postnatal pigs. Notably, the TU64359 lncRNA might promote distal lung development by up-regulating the heparin-binding epidermal growth factor-like (HB-EGF) expression. Our research provides basic lung development datasets and will accelerate clinical researches of newborn lung diseases with pig models. [ABSTRACT FROM AUTHOR]

Background: Exosomes are extracellular vesicles released by almost all cell types, including cancer cells, into bodily fluids such as saliva, plasma, breast milk, semen, urine, cerebrospinal fluid, amniotic fluid, synovial fluid and sputum. Their key function being intercellular communication with both neighbouring as well as distant cells. Cancer exosomes have been shown to regulate organ-specific metastasis. However, little is known about the functional differences and molecular consequences of normal cells responding to exosomes derived from normal cells compared to those derived from cancer cells. Methods: Here, we characterised and compared the transcriptome profiles of primary human normal oral keratinocytes (HNOK) in response to exosomes isolated from either primary HNOK or head and neck squamous cell carcinoma (HNSCC) cell lines. Results: In recipient HNOK cells, we found that regardless of normal or cancer derived, exosomes altered molecular programmes involved in matrix modulation (MMP9), cytoskeletal remodelling (TUBB6, FEZ1, CCT6A), viral/dsRNA-induced interferon (OAS1, IFI6), anti-inflammatory (TSC22D3), deubiquitin (OTUD1), lipid metabolism and membrane trafficking (BBOX1, LRP11, RAB6A). Interestingly, cancer exosomes, but not normal exosomes, modulated expression of matrix remodelling (EFEMP1, DDK3, SPARC), cell cycle (EEF2K), membrane remodelling (LAMP2, SRPX), differentiation (SPRR2E), apoptosis (CTSC), transcription/translation (KLF6, PUS7). We have also identified CEP55 as a potential cancer exosomal marker. Conclusions: In conclusion, both normal and cancer exosomes modulated unique gene expression pathways in normal recipient cells. Cancer cells may exploit exosomes to confer transcriptome reprogramming that leads to cancer-associated pathologies such as angiogenesis, immune evasion/modulation, cell fate alteration and metastasis. Molecular pathways and biomarkers identified in this study may be clinically exploitable for developing novel liquid-biopsy based diagnostics and immunotherapies. [ABSTRACT FROM AUTHOR]

We have developed an approach to facilitate the use of model organism microarrays in related, nonmodel organisms. We demonstrate the method by using Arabidopsis oligonucleotide microarrays to analyze gene expression in Brassica Probes with low hybridization signals to Brassica genomic DNA were excluded from the transcriptional analysis of an Arabidopsis microarray at the software level, forming a virtual Brassica microarray. We then performed an experiment on transcriptional responses during seed germination in Brassica using 17 886 homologous probesets of the virtual array where Brassica mRNA hybridization was detected. We subjected seed to hydration or priming (a step to improve germination vigor) and subsequent heating and drying treatments (steps to prolong shelf life of dried seed). Exploration of the microarray results indicated two likely expression patterns shared by many genes. One class of transcripts was strongly, globally, and irreversibly downregulated by priming, while other transcripts were induced, but often reversibly. Legacy seed‐storage protein messages were in the first class, and many protein synthesis components and some resource mobilization enzymes were in the second. We were able to validate our results by confirming transcriptional responses using reverse transcription polymerase chain reaction (RT–PCR). [ABSTRACT FROM AUTHOR]

Summary Systemic infections of plants by viruses require that viruses modify host cells in order to facilitate infections. These modifications include induction of host factors required for replication, propagation and movement, and suppression of host defense responses, which are likely to be associated with changes in host gene expression. Past studies of the effects of viral infection on gene expression in susceptible hosts have been limited to only a handful of genes. To gain broader insight into the responses elicited by viruses in susceptible hosts, high-density oligonucleotide probe microarray technology was used. Arabidopsis leaves were either mock inoculated or inoculated with cucumber mosaic cucumovirus, oil seed rape tobamovirus, turnip vein clearing tobamovirus, potato virus X potexvirus, or turnip mosaic potyvirus. Inoculated leaves were collected at 1, 2, 4, and 5 days after inoculation, total RNA was isolated, and samples were hybridized to Arabidopsis GeneChip microarrays (Affymetrix). Microarray hybridization revealed co-ordinated changes in gene expression in response to infection by diverse viruses. These changes include virus-general and virus-specific alterations in the expression of genes associated with distinct defense or stress responses. Analyses of the promoters of these genes further suggest that diverse RNA viruses elicit common responses in susceptible plant hosts through signaling pathways that have not been previously characterized. [ABSTRACT FROM AUTHOR]

Unlike other poultry, parent pigeons produce "pigeon milk" in their crops to nurture their squabs, which is mainly controlled by prolactin (PRL). Exception for PRL , the pituitary gland may also release various other peptide and protein hormones. However, whether these hormones change during pigeon crop lactation and their potential physiological functions remain unclear. Here, to identify potential peptide or protein hormone genes that regulate crop lactation, we conducted transcriptome analysis of pigeon pituitary glands at 3 different breeding stages (the ceased stage—nonincubation and non-nurturing stage, the 11th d of the incubation, and the 1st d of the nurturing stage) using RNA sequencing (RNA-Seq). Our analysis identified a total of 15,191 mRNAs and screened out 297 differentially expressed genes (DEG), including PRL, VIP , etc. The expression abundance of PRL mRNA on the 1st d of the nurturing stage was respectively 4.93 and 3.62 folds higher when compared to the ceased stage and the 11th d of the incubation stage. Additionally, the expression abundance of VIP is higher in the 1st d of the nurturing stage than in the ceased stage. Protein–protein interaction (PPI) network and Molecular Complex Detection (MCODE) analysis identified several vital DEGs (e.g., GHRHR, VIP , etc.), being closely linked with hormone and enriched in neuropeptide signaling pathway and response to the hormone. Expression pattern analysis revealed that these DEGs exhibited 4 distinct expression patterns (profile 10, 16, 18, 19). Genes in profile 10 and 19 presented a trend with the highest expression level on 1st d of the nurturing stage, and functional enrichment analysis indicated that these genes are involved in neuropeptide hormone activity, receptor-ligand activity, and the extracellular matrix, etc. Taken together, being consistent with PRL, some genes encoding peptide and protein hormones (e.g., VIP) presented differentially expressed in different breeding stages. It suggests that these hormones may be involved in regulation of the crop lactation process or corresponding behavior in domestic pigeons. The results of this study help to gain new insights into the role of pituitary gland in regulating pigeon lactation. [ABSTRACT FROM AUTHOR]

The Tetratricopeptide repeat (TPR)-like superfamily with TPR conserved domains is widely involved in the growth and abiotic stress in many plants. In this report, the gene MdTPR16 belongs to the TPR family in apple (Malus domestica). Promoter analysis reveal that MdTPR16 incorporated various stress response elements, including the drought stress response elements. And different abiotic stress treatments, drought especially, significantly induce the response of MdTPR16. Overexpression of MdTPR16 result in better drought tolerance in apple and Arabidopsis by up-regulating the expression levels of drought stress-related genes, achieving a higher chlorophyll content level, more material accumulation, and overall better growth compared to WT in the drought. Under drought stress, the overexpressed MdTPR16 also mitigate the oxidative damage in cells by reducing the electrolyte leakage, malondialdehyde content, and the H 2 O 2 and O 2 − accumulation in apples and Arabidopsis. In conclusion, MdTPR16 act as a beneficial regulator of drought stress response by regulating the expression of related genes and the cumulation of reactive oxygen species (ROS). • MdTPR16 positively regulates drought tolerance in apple seedlings. • The MdTPR16 gene enhances plant resistance by inducing the expression of drought-related genes. • After drought stress, the MdTPR16 gene reduces ROS accumulation in plants. • MdTPR16 may be used in the future to breeding drought-resistant varieties. [ABSTRACT FROM AUTHOR]

The aims of this study were to investigate the pathways which dietary nickel chloride (NiCl 2 ) affects small intestine apoptosis in broiler chickens by observing the ultrastructure, and bcl-2, bax, and caspase-3 protein expression and mRNA expression, and cytochrome C, bak and caspase-9 mRNA expression of the small intestine. A total of 240 one-day-old avian broilers were divided into four groups and fed a corn-soybean basal diet as the control diet or three experimental diets supplemented with 300, 600, and 900 mg/kg of NiCl 2 for 42 days. Ultrastructurally, the microvilli were apparently exfoliated, and the mitochondria were swollen and the number of lysosomes increased in the intestinal cells of three experimental groups. As measured by TUNEL and flow cytometry (FCM), the percentage of apoptotic cells in the small intestine and the lymphocytes in the ileum were significantly increased in three experimental groups when compared with those of the control group. Meanwhile, immunohistochemistry, quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme-linked immuno-sorbent assay (ELISA) tests showed that the protein expression, mRNA expression levels were decreased in the bcl-2, whereas those of bax and caspase-3, and the cytochrome C, bak and caspase-9 mRNA expression levels were increased in three experimental groups. The abovementioned results show that pathway of dietary NiCl 2 -induced small intestine apoptosis is related to the mitochondrial damage and promotion of the cytochrome C release from mitochondria, which activates the mitochondrion-mediated apoptosis pathway. [ABSTRACT FROM AUTHOR]

Abstract: Airway mucus overproduction is a cardinal feature of airway inflammatory diseases, such as chronic obstructive pulmonary disease and cystic fibrosis. Since the small G-protein Ras is known to modulate cellular functions in the lung, we sought to investigate whether the Ras inhibitor simvastatin could attenuate acrolein-induced mucin production in rat airways. Rats were exposed to acrolein for 12days, after first being pretreated intragastrically for 24h with either simvastatin alone or simvastatin in combination with mevalonate, which prevents the isoprenylation needed for Ras activation. Lung tissue was analyzed for extracellular signal-regulated kinase (ERK) activity, goblet cell metaplasia and mucin production. To analyze the effect of simvastatin on mucin production in more detail, acrolein-exposed human airway epithelial NCI-H292 cells were pretreated with simvastatin alone or together with mevalonate. Culture medium was collected to detect mucin secretion, and cell lysates were examined for Ras-GTPase activity and epidermal growth factor receptor (EGFR)/ERK phosphorylation. In vivo, simvastatin treatment dose-dependently suppressed acrolein-induced goblet cell hyperplasia and metaplasia in bronchial epithelium and inhibited ERK phosphorylation in rat lung homogenates. Moreover, simvastatin inhibited Muc5AC mucin synthesis at both the mRNA and protein levels in the lung. In vitro, simvastatin pretreatment attenuated the acrolein-induced significant increase in MUC5AC mucin expression, Ras-GTPase activity and EGFR/ERK phosphorylation. These inhibitory effects of simvastatin were neutralized by mevalonate administration both in vitro and in vivo. Our results suggest that simvastatin may attenuate acrolein-induced mucin protein synthesis in the airway and airway inflammation, possibly by blocking ERK activation mediated by Ras protein isoprenylation. Thus, the evidence from the experiment suggests that human trials are warranted to determine the potential safety and efficacy of simvastatin for treatment of over production of airway mucus. [Copyright &y& Elsevier]

Pseudorabies virus glycoprotein E (PRV gE) has been recognized as a suitable diagnostic antigen for pseudorabies. In order to produce gE antigen in large quantities and at low cost, a gene fragment encoding PRV gE epitopes was expressed in Pichia pastoris expression system. SDS-PAGE and Western blotting revealed that the expression product was two recombinant proteins, approximately 38 and 32 kDa, in the culture supernatant of P. pastoris integrant 72 h after induction. Protein concentration assay showed the expression product amounted to 106.7 mg/l, accounting for 66.67% of total culture supernatant proteins. An indirect PRV gE-ELISA was then established by using the recombinant expression product as a coating antigen. Cross-reactivity assay showed that this antigen was PRV specific. Reproducibility experiment displayed good consistency. Comparison of detection results of 348 field serum samples between PRV gE-ELISA and a commercially available PRV diagnostic kit showed there was no significant difference between these two methods (P>0.05). [Copyright &y& Elsevier]

Differential display analysis by cDNA fractionation, collection of differentially expressed fractions of interests and their downstream characterization is demonstrated. cDNA pools from two strains of Cochliobolus heterostrophus fungus were generated by specific restriction digestion and selective ligation. Micropreparative separation and isolation of differentially expressed transcript representatives were accomplished by high-performance capillary gel electrophoresis. The collected individual DNA molecules were polymerase chain reaction amplified and sequenced to create expressed sequence tags for the genes of interests. High resolving power and sensitivity of capillary gel electrophoresis enabled fast and automated processing of minute amounts of cDNA samples with high precision. [Copyright &y& Elsevier]

Light is a key environmental factors affecting anthocyanin accumulation in plants. Ubiquitin E3 ligase COP1 has been proved to be a negative regulator involved in light-regulated plant development process, whereas the function and expression specificity of COP1 in anthocyanin biosynthesis in sweet cherry remains unclear. In the present study, we identified a COP1 in sweet cherry, named PacCOP1 , it exhibited apparent different expression patterns in red-colored 'Hongdeng' and bi-colored 'Satonishiki', with increasing trend largely in 'Satonishiki', but decreasing trend in 'Hongdeng' after veraison, which was contrary to their variation tendency of anthocyanin content. While the expression abundance of anthocyanin biosynthesis related genes were largely increased after veraison, in accordance with anthocyanin content. Correlation analysis proved that the expression of PacCOP1 was negative correlated with the major genes on anthocyanin accumulation in 'Hongdeng' and 'Satonishiki' fruit, in especial Pac DFR, Pac ANS, Pac MYBA and Pac bHLH33. Furthermore, over-expression of PacCOP1 in Arabidopsis displayed increased COP1 transcript level with negligible pigmentation and corresponding lower expression level of AtPAP1 , AtDFR , AtLDOX , and AtUFGT. These results revealed the negative regular role of PacCOP1 in anthocyanin biosynthesis by repressing the PacMYBA transcription level, followed by down-regulating the structural genes expression abundance, eventually leading to attenuated anthocyanin accumulation in fruits. • A novel Ubiquitin E3 ligase gene COP1 was identified from sweet cherry, named PacCOP1. • PacCOP1 exhibited apparent different expression patterns in red- and bi-colored cultivars, contrary to that of anthocyanin content. • The expression level of PacCOP1 was negative correlated with mRNA abundance of Pac DFR, Pac ANS, Pac MYBA and Pac bHLH33. [ABSTRACT FROM AUTHOR]